update docs

shenwei356 · Nov 2, 2016 · c01e3dc · c01e3dc
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diff --git a/README.md b/README.md
@@ -1,5 +1,11 @@
-# TaxonKit - NCBI Taxonomy Toolkit
+# TaxonKit - Crossplatform and Efficient NCBI Taxonomy Toolkit
 
+**Documents:** [http://bioinf.shenwei.me/taxonkit](http://bioinf.shenwei.me/taxonkit)
+([**Usage**](http://bioinf.shenwei.me/taxonkit/usage/))
+
+**Source code:** [https://github.com/shenwei356/taxonkit](https://github.com/shenwei356/taxonkit)
+[![GitHub stars](https://img.shields.io/github/stars/shenwei356/taxonkit.svg?style=social&label=Star&?maxAge=2592000)](https://github.com/shenwei356/taxonkit)
+[![license](https://img.shields.io/github/license/shenwei356/taxonkit.svg?maxAge=2592000)](https://github.com/shenwei356/taxonkit/blob/master/LICENSE)
 
 **Latest version:** [![Latest Version](https://img.shields.io/github/release/shenwei356/taxonkit.svg?style=flat?maxAge=86400)](https://github.com/shenwei356/taxonkit/releases)
 [![Github Releases](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/total.svg?maxAge=3600)](http://bioinf.shenwei.me/taxonkit/download/)

diff --git a/doc/docs/download.md b/doc/docs/download.md
@@ -18,10 +18,6 @@ Links:
     [taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_linux_386.tar.gz)
     - [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_linux_amd64.tar.gz)
     [taxonkit_linux_amd64.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_linux_amd64.tar.gz)
-    - [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_linux_arm.tar.gz)
-    [taxonkit_linux_arm.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_linux_arm.tar.gz)
-    - [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_linux_arm64.tar.gz)
-    [taxonkit_linux_arm64.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_linux_arm64.tar.gz)
 - **Mac OS X**
     - [![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_darwin_386.tar.gz)
       [taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1/taxonkit_darwin_386.tar.gz)
@@ -65,28 +61,26 @@ For Go developer, just one command:
 
 ## Previous Versions
 
--
+
 
 
 <div id="disqus_thread"></div>
 <script>
+
 /**
-* RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
-* LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables
-*/
+*  RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
+*  LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
 /*
 var disqus_config = function () {
-this.page.url = PAGE_URL; // Replace PAGE_URL with your page's canonical URL variable
+this.page.url = PAGE_URL;  // Replace PAGE_URL with your page's canonical URL variable
 this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
 };
 */
 (function() { // DON'T EDIT BELOW THIS LINE
 var d = document, s = d.createElement('script');
-
 s.src = '//taxonkit.disqus.com/embed.js';
-
 s.setAttribute('data-timestamp', +new Date());
 (d.head || d.body).appendChild(s);
 })();
 </script>
-<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript" rel="nofollow">comments powered by Disqus.</a></noscript>
+<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -61,7 +61,7 @@ Flags:
 
 Examples
 
-1. default usage
+1. Default usage
 
         $ taxonkit list --nodes nodes.dmp --ids 9605
         9605
@@ -70,7 +70,7 @@ Examples
             741158
           1425170
 
-1. change ident, the list could be used to extract sequences from BLAST database with `blastdbcmd`
+1. Removing indent. The list could be used to extract sequences from BLAST database with `blastdbcmd`
 
         $ taxonkit list --nodes nodes.dmp --ids 9605 --indent ""
         9605
@@ -79,7 +79,16 @@ Examples
         741158
         1425170
 
-1. adding names
+    **Performance:** Time and memory usage for whole taxon tree:
+
+        $ # emptying the buffers cache
+        $ su -c "free && sync && echo 3 > /proc/sys/vm/drop_caches && free"
+
+        $ memusg -t taxonkit list --nodes nodes.dmp --ids 1 --indent "" > t0.txt
+        elapsed time: 2.987s
+        peak rss: 82.79 MB
+
+1. Adding names
 
         $ taxonkit list --nodes nodes.dmp --names names.dmp --ids 9605
         9605 [genus] Homo
@@ -88,27 +97,35 @@ Examples
             741158 [subspecies] Homo sapiens ssp. Denisova
           1425170 [species] Homo heidelbergensis
 
+    **Performance:** Time and memory usage for whole taxon tree:
+
+        $ # emptying the buffers cache
+        $ su -c "free && sync && echo 3 > /proc/sys/vm/drop_caches && free"
+
+        $ memusg -t taxonkit list --nodes nodes.dmp --names names.dmp --ids 1 > t1.txt
+        elapsed time: 9.825s
+        peak rss: 648.65 MB
+
+
 
 
 <div id="disqus_thread"></div>
 <script>
+
 /**
-* RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
-* LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables
-*/
+*  RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
+*  LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
 /*
 var disqus_config = function () {
-this.page.url = PAGE_URL; // Replace PAGE_URL with your page's canonical URL variable
+this.page.url = PAGE_URL;  // Replace PAGE_URL with your page's canonical URL variable
 this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
 };
 */
 (function() { // DON'T EDIT BELOW THIS LINE
 var d = document, s = d.createElement('script');
-
-s.src = '//csvtk.disqus.com/embed.js';
-
+s.src = '//taxonkit.disqus.com/embed.js';
 s.setAttribute('data-timestamp', +new Date());
 (d.head || d.body).appendChild(s);
 })();
 </script>
-<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript" rel="nofollow">comments powered by Disqus.</a></noscript>
+<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
diff --git a/doc/site b/doc/site
diff --git a/taxonkit/cmd/root.go b/taxonkit/cmd/root.go
@@ -39,6 +39,7 @@ Version: %s
 Author: Wei Shen <shenwei356@gmail.com>
 
 Source code: https://github.com/shenwei356/taxonkit
+Documents  : http://bioinf.shenwei.me/taxonkit
 
 Dataset:
 

diff --git a/taxonkit/main.go b/taxonkit/main.go
@@ -22,6 +22,7 @@ package main
 
 import (
 	"os"
+	// "runtime/pprof"
 
 	"github.com/op/go-logging"
 	"github.com/shenwei356/taxonkit/taxonkit/cmd"
@@ -39,8 +40,15 @@ func init() {
 }
 
 func main() {
+	// go tool pprof ./taxonkit pprof
 	// f, _ := os.Create("pprof")
 	// pprof.StartCPUProfile(f)
 	// defer pprof.StopCPUProfile()
+
 	cmd.Execute()
+
+	// go tool pprof --alloc_space ./taxonkit mprof
+	// f2, _ := os.Create("mprof")
+	// pprof.WriteHeapProfile(f2)
+	// defer f2.Close()
 }